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I almost never use Master Balls on Shinies. When it comes to them I usually try an Ultra Ball and call it good, because usually it is!
I always use them on Legendaries. I don't have to battle them, which makes my life easier, and I get the Pokemon no matter what.

I never use the master ball on legendaries unless it's a roamer and I get tired of chasing it around. Generally I save my master balls for shiny pokemon who I think might be able to use Roar or Whirlwind or Explosion or whatever.

Never use Master Ball on a legendary, since I can usually easily reset if something happens. I save mine for trouble shinies, like a random exploder or roarer when I don't have the right Pokémon with me or a shiny who's hurting themselves/poisoned/burned/using struggle/being hit by weather effects etc. Only time I ever used a Master Ball on a legend was Latias in Sapphire (lazy) and I used my first ever Master Ball on a regular Wailord, oh shame...

There's no real point in using them on legendaries, since you can save before battling them and reset if you happen to run out of Poke Balls. So I'd save mine on the off chance that I run across a shiny and can't quite manage to catch it otherwise. Of course, that depends entirely on the shiny, considering there's a good chunk of them that have such hideous colour combinations that I wouldn't bother to catch them anyway. /picky pants

Use the master ball as you please, it doesn't matter whether or not if it's a shiny. I would use it on a super rare one, of a Pokemon I like, of a shiny legendary (if it's possible to have a legitimate one).

I'd much rather catch a legendary with a master ball. Shiny Pokemon is not exactly something I seek and I usually catch regular wild Pokemon with a quick ball, great ball, or timer ball without weakening it.

If I saw a shiny roaming pokemon I would, just because I would be too scared of trying to weaken it thinking I might accidentally kill it.

Or if I saw a shiny legendary and had no other balls left then of course I would use a Master Ball.

I usually never use my Master Ball. I just like having it.

I remember this one time I used a Master Ball on a Magmar in Gold version because I was looking for a Magmar forever to breed for a Magby and when I finally found one I realized all I had was a Master Ball. So I threw it. My friends thought I was crazy for doing that.

I always regret using the masterball. Like just recently in Heart Gold I used the masterball on Ho-Oh and immediately regretted it because I'd much rather use the masterball on Suicine. But if I had a masterball when a shiny came along and it was one of my favorite Pokemon, I may use it. Maybe. Not sure, I've never been in that situation

Oh my gosh. You can tell I havent been on here since before X & Y was released.... Signature was before fairy type was even confirmed. Oh lordy that's been awhile ago.

Hmm. tough call! Normally I'd use a Master Ball on a roaming Legendary, just to aviod a headache of trying to catch one without it running away. But I would use one if the shiny was going to be a pain to capture(like if my pokemon were overpowered and did not have false swipe/any non KO'ing move).